The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_206933.4(USH2A):c.1966G>A (p.Asp656Asn)

CA143431

48481 (ClinVar)

Gene: USH2A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: a5c58407-b571-46b2-b787-30711d1fd9f3
Approved on: 2020-05-25
Published on: 2020-05-26

HGVS expressions

NM_206933.4:c.1966G>A
NM_206933.4(USH2A):c.1966G>A (p.Asp656Asn)
NC_000001.11:g.216289285C>T
CM000663.2:g.216289285C>T
NC_000001.10:g.216462627C>T
CM000663.1:g.216462627C>T
NC_000001.9:g.214529250C>T
NG_009497.1:g.139112G>A
NG_009497.2:g.139164G>A
NM_007123.5:c.1966G>A
NM_206933.2:c.1966G>A
NM_206933.3:c.1966G>A
NM_007123.6:c.1966G>A
ENST00000307340.7:c.1966G>A
ENST00000366942.3:c.1966G>A
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Likely Benign

Met criteria codes 2
BP4 BS1_Supporting
Not Met criteria codes 1
PM3

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The allele frequency of the c.1966G>A (p.Asp656Asn) variant in USH2A is 0.095% (16/10466 CI 95%) of Finnish alleles in gnomAD v3., which is a higher frequency than would be expected for an autosomal recessive pathogenic variant based on the thresholds defined by the ClinGen Hearing Loss Expert Panel (BS1_Supporting). The variant has been identified in 3 probands with hearing loss and 2 probands with Usher syndrome (SCV000065500.6; PMID: 16963483); however an alternate cause of hearing loss in other genes was identified in 3 probands (SCV000065500.6), and a second variant in USH2A was not identified in the other two probands (SCV000065500.6; PMID: 16963483). Finally, in the last proband, another likely benign variant was identified with phasing unknown (SCV000065500.6). Altogether, this evidence does not meet the criteria set to apply PM3_Supporting. Additionally, computational prediction analysis using the metapredictor tool REVEL suggests that the variant may not impact the protein (BP4). In summary, the c.1966G>A (p.Asp656Asn) variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BS1_Supporting, BP4.
Met criteria codes
BP4
REVEL: 0.073
BS1_Supporting
Present in 0.09746% (145/129044 CI 95%) non-Finnish European alleles in gnomAD v2.1.1 0.09589% (16/10466 CI 95%) of Finnish alleles in gnomAD v3
Not Met criteria codes
Curation History
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